Fragment-Based Drug Discovery

From Hits to Leads and Lessons Learned

April 22-23, 2015

A mutli-disciplinary gathering where you can gain new insights and refresh on new ideasthrough networking and presentations

Djamal B., Arisan Therapeutics

Fragment-based approaches to find new small molecule drug candidates are now part of most drug discovery campaigns. The challenge of fragment-based drug design campaigns has always been progressing fragment hits against the target compound to obtaining a clinical candidate. Via case studies on success stories and compounds moving forward or not in preclinical development, this conference will highlight best practices and pitfalls to avoid. Join fellow drug discovery colleagues for this day-and-a-half meeting in the second half of CHI’s larger Drug Discovery Chemistry event.

Small molecule inhibitors targeting the deubiquitinase Ubiquitin Specific Protease 7 (USP7) have potential as cancer therapeutics. Using ligand-based NMR in an activity agnostic FBLD effort, we have identified binders to several sites in USP7 including a unique site in the “palm” of USP7. These could be shown to be active. The palm series imply a very distinct mechanism of action independent of the catalytic triad by binding in a region involved in USP7-Ubiquitin interaction.

We developed a new technology in which weakly bound electrophilic drug-like fragments are irreversibly trapped on the catalytic or non-catalytic cysteines of protein targets. Subsequent intact protein MS can be used to identify fragment hits, allowing one to screen 100 or more fragments/day without the use of special robotic equipment. The developed technology can be used to discover covalent drug leads for enzyme inhibitors and protein-protein interaction inhibitors.

The aberrant formation of the β-catenin/T cell factor (Tcf) complex in the canonical Wnt signaling pathway has been recognized as the major driving force for many cancers and fibroses. Crystallographic and biochemical analyses reveal that the binding modes of Tcf, cadherin and adenomatous polyposis coli (APC) with β-catenin are identical. By using a fragment hopping technique, we have successfully designed and synthesized potent small-molecule β-catenin/Tcf inhibitors with high selectivities over β-catenin/cadherin and β-catenin/APC interactions.

3:10 The Application of Extended Huckel Theory for Pharmacophore Modeling

Pharmacophore models play an essential role in drug discovery. Generating pharmacophore models which encode accurate molecular recognition features are highly dependent on properly defined annotation points. Here we have developed a new approach for pharmacophore modeling which is based on a semi-empirical method using Extended Hückel Theory (EHT). The pharmacophore features generated through the EHT annotation scheme take into account ligand resonance and electron withdrawing effects and are sensitive to non-standard interactions, such as C-H and halogen bond interactions, during pharmacophore screening.

Kinetic Target-Guided Synthesis (TGS) has been developed, in which the biological target is actively engaged in the irreversible assembly of its own inhibitory ligand from a library of reactive fragments. The Manetsch laboratory developed the first kinetic TGS approach for the identification of compounds disrupting protein-protein interactions. We demonstrated that the sulfo-click reaction, an amidation reaction between thio acids and sulfonyl azides, is suitable for a kinetic TGS approach targeting proteins of the Bcl-2 family.

In this session, attendees choose a specific roundtable discussion to join. Each group has a moderator to ensure focused conversations around key issues within the topic. The small group format allows participants to informally meet potential collaborators, share examples from their work and discuss ideas with peers. Check our website in February to see the full listing of breakout topics and moderators.

Fragment-based discovery has now been successfully established as an alternative approach to HTS and has produced multiple drug candidates that are in clinical trials. Some of the appealing features of the approach include the ability to efficiently sample chemical space and to produce drug candidates that have superior physicochemical properties. In this talk I will provide a perspective on how Fragment-Based drug discovery evolved over the last 15 years and challenged conventional thinking in Drug Discovery.

9:30 Coffee Break in the Exhibit Hall with Poster Viewing

Best Practices, Advances and Challenges in Fragment-Based Discovery

10:10 Chairperson’s Remarks

Roderick E. Hubbard, Ph.D., Director, Chemistry, Vernalis Research and University of York

This presentation will outline our approach to fragment library design and how we have incorporated descriptors of shape and complexity to complement more traditional approaches. I will also describe our approach to targeting several GTPases implicated in cancer.

As opposed to focusing on desirable properties for a library (shape, physical properties, etc), the more novel design principles applied to the library will be described. Namely, 1) an integrated chemogenomics database of internal and external data was used to identify biologically privileged motifs for incorporation in the library, 2) library members and expansion analogues were selected based on a “diversified portfolio” approach to fragment hit follow up as opposed to the more standard nearest neighbor follow-up, and 3) visualization tools were built to empower medicinal chemists to readily use these guiding principles to select (or design) fragments that fulfilled these goals.

SPR has become the workhorse method for rapid and accurate fragment screening. We present results from a collaborative effort between the Hopkins-Navratilova lab and GE Healthcare prototyping new assays methods and new technology to advance SPR fragment screening. We will introduce the first results on a new, prototype Biacore™ instrument.

The Astex library has been through multiple rounds of enhancement since the last publication. Armed with thousands of proprietary protein-fragment crystal structures, across a wide range of protein families generated over 10 years, we will discuss how later iterations of the fragment library have been constructed and analysed. We will show how the fragment hit rate varies with lipophilicity and heavy atom count, and compare the hit rates of 2D versus 3D fragments. We will also present a recently disclosed initiative involving minimal binding pharmacophore elements that are appropriate for fragments and show how they have been used to drive library enhancement. These privileged pharmacophores have added value by generating novel fragment hits for progression into hit to lead chemistry.

FBDD relies on the premise that the binding mode of fragments is conserved upon expansion to a ligand. This hypothesis is frequently tested by deconstructing ligands into their fragments, and by determining whether the fragments still bind, and if they do, whether their locations are conserved. We show that a condition for fragment conservation can be developed in terms of binding hot spots, i.e., regions of the protein where interactions with any ligand contribute a large fraction of the binding free energy. The condition can be used to predict fragment size and shape in a library to be screened for a specific target, including non-traditional PPI targets and proteins that can be targeted only by macrocycles.

12:30 Walk and Talk Luncheon in the Exhibit Hall with Poster Viewing (last chance for viewing) and Poster Awards

ABT-263 (navitoclax) is a potent inhibitor of the anti-apoptotic proteins BCL-XL and Bcl-2 and has proven effective against several types of B-cell derived cancers. However, thrombocytopenia driven by BCL-XL inhibition has been dose-limiting for navitoclax in the single agent setting. In attempt to overcome this side effect we have employed fragment-based methods to obtain a BCL-2 selective compound which could serve as a starting point for the development of a BCL-2 selective anti-cancer agent. Such an agent would potentially overcome the BCL-XL mediated thrombocytopenia observed with ABT-263. In addition, fragment screening methods and structural biology have been used to drive discovery of novel inhibitors for the pro-survival protein MCL-1. MCL-1 has been shown to be a resistance factor for ABT-263. Cores derived from a biphenyl sulfonamide and salicylic acid were uncovered in an NMR-based fragment screen and elaborated using high throughput analog synthesis. This culminated in the discovery of selective and potent inhibitors of MCL-1 that may serve as promising leads for medicinal chemistry optimization efforts.

2:15 Choosing and Using Fragments in Oncology Lead Discovery

Roderick E. Hubbard, Ph.D., Director, Chemistry, Vernalis Research and University of York

Fragment methods have been used successfully for many oncology targets – to assess ligandability, to provide chemical tools to probe and validate target biology, and to generate candidates to progress into clinical trials. I will review some of our recent experiences in using fragments for lead and candidate discovery, with particular emphasis on the very early stages of developing fragment and early hit SAR to decide on which series to progress.

Inhibitors of Mycobacterium tuberculosis BioA with high ligand efficiency have been identified by screening for compound-induced Tm shifts with Differential Scanning Fluorimetry (DSF). Structures with bound fragments sample an ensemble of different active site conformations that correlate with ligand binding. DSF shows that some of the ligands destabilize protein folding, while others are stabilizing, even though dissociation constants obtained by ITC are similar. Destabilizing ligands should not be ignored when searching for lead compounds.

3:30 Use of FBDD in the Discovery of Two Series of Potent Methionine Aminopeptidase-2 Inhibitors

Chris McBride, Staff Scientist, Medicinal Chemistry, Takeda

This presentation will demonstrate the strategy used to identify two series of methionine aminopeptidase-2 (MetAP2) inhibitors. Fragment libraries were screened for hits with high ligand-efficiency (LE) and orthogonal hit confirmation led to a low affinity indazole core being selected for directed elaboration with the aid of structural information. Additionally, structural insight and SAR from the indazole series led to the design and accelerated knowledge-based fragment growth of the pyrazolo[4,3-b]indoles as MetAP2 inhibitors.

4:00 FBDD on Metalloprotein Targets

Seth M. Cohen, Ph.D., Professor, Department of Chemistry and Biochemistry, University of California, San Diego

Most inhibitors of alloproteins employ a functional group that binds to the active site metal ion. We have developed an FBDD approach to metalloenzyme inhibitors by developing a library of suitable metal-binding pharmacophores (MBPs). Thermodynamic and structural investigations are being used to provide insight into the influence of the protein active site on MBP binding. In this presentation, our efforts on utilizing these MBPs for metalloprotein inhibition will be discussed.